Lignocellulosic biomass represents a vast resource for the production of renewable transportation fuels and chemicals to offset and replace current fossil fuel usage. For many decades, worldwide research efforts have focused on the development of cost-effective processes to selectively convert the polysaccharide components of plant cell walls, namely cellulose and hemicellulose, to fuels and chemicals through biological and chemical pathways. For example, in bioethanol production, biomass typically undergoes a mild thermochemical pretreatment step followed by enzymatic hydrolysis and fermentation to produce ethanol from the monomeric components of both cellulose and hemicellulose.
The lignin component of lignocellulosic biomass is an energy-dense, heterogeneous alkyl-aromatic polymer constructed from phenylpropanoid monomers used by plants for water transport and defense, and it is the second most abundant biopolymer on Earth after cellulose. Lignin is typically underutilized in most selective conversion processes for biofuel production. In the production of fuels and chemicals from biomass, lignin is typically burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively upgrade the monomers to value added products. This limited ability to utilize lignin, despite being the most energy dense polymer in the plant cell wall, is primarily due to its inherent heterogeneity and recalcitrance. Despite having a longer history of use as alternative renewable raw materials, cellulose and hemicellulose still remain important, high volume, readily available renewable raw materials, and next generation technologies that process these polysaccharides efficiently and economically are still needed. Thus, compositions, methods, and processes that can simultaneously and/or in parallel convert all of the substituent components of biomass, e.g. lignin, cellulose, and hemicellulose, to useful chemical intermediates, final chemical products (including fuels), is highly desirable to make steps towards lessening global dependency on petroleum.
However, in order to displace our current petrochemical consumption, an expanded renewable product slate is necessary, similar to the myriad of products currently derived from crude petroleum. This requires efficient and economically viable technology for converting all of the main constituents of biomass, cellulose, hemicellulose, as well as lignin, to useful final products, as well as chemical intermediates that can be converted to useful final products, utilizing either new technologies or existing technologies. The present application provides a suite of innovative technologies that may serve as cornerstones for future biomass-to-chemicals manufacturing plants, wherein these technologies focus on the first task of converting biomass to cis, cis-Muconic acid (hereinafter referred to as “muconic acid”), followed by the second task of converting the muconic acid to useful products including, but not limited to, adipic acid, 1,6-hexanediol, and hydrocarbon fuels.
Genetic engineering of microbial organisms is most commonly known due to the landmark Supreme Court case of Diamond v. Chakrabarty, wherein the court validated Chakrabarty's U.S. Pat. No. 4,259,444, directed to a Pseudomonas putida strain that had been engineered to degrade various oil derivatives, including octane and naphthalene.
Since then, researchers have pursued engineered microorganisms for biologically converting various biomass components to numerous chemical intermediates and products, including muconic acid, followed by conversion to adipic acid. Annual world-wide production of adipic acid in 1989 was estimated at 4.2 billion pounds and production has continued to grow since then. With U.S. production at 1.75 billion pounds in 1992, adipic acid consistently ranks as one the top fifty chemicals produced domestically. Nearly 90% of domestic adipic acid is used to produce nylon-6,6. Other uses for adipic acid include production of lubricants and plasticizers. Thus, there is a large economic driver behind the development of improved methods for muconic acid production, especially for the development of improved production methods that utilize renewable resources.
For example Koppisch et al. (“Koppisch”) describe the use of engineered prokaryotic organisms for converting D-glucose to catechol and muconic acid (WO 2012/106257). This includes the introduction of exogenous decarboxylase genes, including aroY from Klebsiella pneumoniae, and the introduction of exogenous dioxygenase genes for converting catechol to muconic acid, for example catA.
U.S. Pat. No. 5,487,987 to Frost et al. (“Frost”) describes the production of adipic acid through a metabolic pathway producing the cis, cis-muconic acid intermediate, also utilizing D-glucose as the starting material, and Escherichia coli genetically engineered to include genes endogenous to Klebsiella pneumoniae and Acinetobacter calcoaceticus. 
Burk et al. (“Burk”) describes the use of engineered microbial microorganisms to produce terephthalate through a muconic acid intermediate comprising trans,trans-muconate and/or cis, trans-muconate, starting with succinyl-CoA as a starting material (WO 2011/017560).
U.S. Pat. No. 8,133,704 to Baynes et al. (“Baynes”) describes the use of genetically engineered microorganisms including E. coli, C. glutanicum, B. flavum, and B. lactofermentum for the eventual production of adipic acid, utilizing carbohydrate starting materials.
Weber et al. describe a genetically modified Saccharomyces cerevisiae to produce cis, cis-muconic acid utilizing aromatic amino acid pathways (Applied and Environmental Microbiology (2012) 78(23), 8421-8430).
Pseudomonas putida has been of particular interest recently, especially since completion of the genomic sequencing of Pseudomonas putida KT2440 (Environmetal Microbiology (2002) 4(12), 799-808). Jimenez et al. have characterized four of the main pathways in the KT2440 strain, including the protocatechuate and catechol branches of the β-ketoadipate pathway, the homogentisate pathway, and the phenylacetate pathway (Environmental Microbiology (2002) 4(12), 824-841).
Even before its genomic sequencing, scientists attempted to use P. putida as an organism for producing muconic acid. For example, U.S. Pat. Nos. 4,480,034 and 4,731,328 describe converting toluene to muconic acid, utilizing engineered microorganisms including Pseudomonas putida. 
More recently, Bang et al. (“Bang”) describe the use of a P. putida strain (BM014) for the production of cis, cis-muconic acid utilizing benzoic acid as a starting material (Journal of Fermentation and Bioengineering (1995) 79(4), 381-383). J. van Duuren et al. describe the use of P. putida KT2440 for the production of cis, cis-muconic acid utilizing benzoate as a starting material (Journal of Biotechnology (2011) 156, 163-172).
Thus, a review of the literature illustrates that a significant need remains for improved, flexible, reliable, economical technologies that are capable of converting a wide variety of biomass to industrially relevant chemical intermediates and final products, especially technologies that are capable of converting all of the key constituents of biomass; e.g. lignin, cellulose, and hemicellulose. To achieve this goal, robust genetically modified microorganisms, and/or mixtures of microorganisms are required that are capable of funneling chemical compounds through multiple metabolic pathways to common a common precursor or precursors, that can be subsequently converted to useful chemical intermediates and final products. In addition, novel upstream and downstream processing techniques are needed to assist with biomass fractionation, lignin and polysaccharide depolymerization, and precursor conversion to chemical intermediates and final products. The concepts presented herein provide some technologies that address these and other needs.